Are there two separate cleanup steps - one at the end of combat (rule 628) and one after combat (rule 519)?

Ruling: There is only one cleanup step. The cleanup mentioned in rule 519 (after combat) is referring to the same cleanup step described in rule 628 (the last substep of combat). The wording in 519 is just imprecise.

Nuances:

• Assault bonuses are removed when Attacking units are recalled and lose Attacker status during the 628 cleanup, as they are no longer on the battlefield
• Shield bonuses are removed because Shield only grants bonuses "while a defender" and Defender status is cleared from units not present during combat, so once combat closes units lose the Shield bonus
• All units at the base heal at end of combat, even if they weren't in the combat